Job ID = 6529337 SRX = SRX1847048 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:12 33320269 reads; of these: 33320269 (100.00%) were unpaired; of these: 1630359 (4.89%) aligned 0 times 21956276 (65.89%) aligned exactly 1 time 9733634 (29.21%) aligned >1 times 95.11% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 10266572 / 31689910 = 0.3240 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 02:01:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:25: 1000000 INFO @ Tue, 30 Jun 2020 02:01:34: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:01:44: 3000000 INFO @ Tue, 30 Jun 2020 02:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 02:01:45: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:01:45: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:01:53: 4000000 INFO @ Tue, 30 Jun 2020 02:01:53: 1000000 INFO @ Tue, 30 Jun 2020 02:02:01: 2000000 INFO @ Tue, 30 Jun 2020 02:02:02: 5000000 INFO @ Tue, 30 Jun 2020 02:02:09: 3000000 INFO @ Tue, 30 Jun 2020 02:02:11: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 30 Jun 2020 02:02:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:02:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:02:17: 4000000 INFO @ Tue, 30 Jun 2020 02:02:19: 7000000 INFO @ Tue, 30 Jun 2020 02:02:24: 1000000 INFO @ Tue, 30 Jun 2020 02:02:25: 5000000 INFO @ Tue, 30 Jun 2020 02:02:28: 8000000 INFO @ Tue, 30 Jun 2020 02:02:32: 6000000 INFO @ Tue, 30 Jun 2020 02:02:33: 2000000 INFO @ Tue, 30 Jun 2020 02:02:37: 9000000 INFO @ Tue, 30 Jun 2020 02:02:39: 7000000 INFO @ Tue, 30 Jun 2020 02:02:42: 3000000 INFO @ Tue, 30 Jun 2020 02:02:46: 8000000 INFO @ Tue, 30 Jun 2020 02:02:46: 10000000 INFO @ Tue, 30 Jun 2020 02:02:52: 4000000 INFO @ Tue, 30 Jun 2020 02:02:53: 9000000 INFO @ Tue, 30 Jun 2020 02:02:56: 11000000 INFO @ Tue, 30 Jun 2020 02:03:00: 10000000 INFO @ Tue, 30 Jun 2020 02:03:01: 5000000 INFO @ Tue, 30 Jun 2020 02:03:05: 12000000 INFO @ Tue, 30 Jun 2020 02:03:07: 11000000 INFO @ Tue, 30 Jun 2020 02:03:09: 6000000 INFO @ Tue, 30 Jun 2020 02:03:13: 13000000 INFO @ Tue, 30 Jun 2020 02:03:14: 12000000 INFO @ Tue, 30 Jun 2020 02:03:17: 7000000 INFO @ Tue, 30 Jun 2020 02:03:21: 14000000 INFO @ Tue, 30 Jun 2020 02:03:21: 13000000 INFO @ Tue, 30 Jun 2020 02:03:25: 8000000 INFO @ Tue, 30 Jun 2020 02:03:28: 14000000 INFO @ Tue, 30 Jun 2020 02:03:29: 15000000 INFO @ Tue, 30 Jun 2020 02:03:34: 9000000 INFO @ Tue, 30 Jun 2020 02:03:35: 15000000 INFO @ Tue, 30 Jun 2020 02:03:37: 16000000 INFO @ Tue, 30 Jun 2020 02:03:42: 10000000 INFO @ Tue, 30 Jun 2020 02:03:42: 16000000 INFO @ Tue, 30 Jun 2020 02:03:46: 17000000 INFO @ Tue, 30 Jun 2020 02:03:49: 17000000 INFO @ Tue, 30 Jun 2020 02:03:50: 11000000 INFO @ Tue, 30 Jun 2020 02:03:55: 18000000 INFO @ Tue, 30 Jun 2020 02:03:57: 18000000 INFO @ Tue, 30 Jun 2020 02:03:58: 12000000 INFO @ Tue, 30 Jun 2020 02:04:03: 19000000 INFO @ Tue, 30 Jun 2020 02:04:05: 19000000 INFO @ Tue, 30 Jun 2020 02:04:06: 13000000 INFO @ Tue, 30 Jun 2020 02:04:11: 20000000 INFO @ Tue, 30 Jun 2020 02:04:12: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:04:14: 14000000 INFO @ Tue, 30 Jun 2020 02:04:19: 21000000 INFO @ Tue, 30 Jun 2020 02:04:19: 21000000 INFO @ Tue, 30 Jun 2020 02:04:22: 15000000 INFO @ Tue, 30 Jun 2020 02:04:23: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:04:23: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:04:23: #1 total tags in treatment: 21423338 INFO @ Tue, 30 Jun 2020 02:04:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:04:23: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:04:23: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:04:23: #1 total tags in treatment: 21423338 INFO @ Tue, 30 Jun 2020 02:04:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:04:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:04:23: #1 tags after filtering in treatment: 21423338 INFO @ Tue, 30 Jun 2020 02:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:23: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:24: #1 tags after filtering in treatment: 21423338 INFO @ Tue, 30 Jun 2020 02:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:04:24: #1 finished! INFO @ Tue, 30 Jun 2020 02:04:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:04:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:04:25: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 02:04:25: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:25: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:04:25: #2 alternative fragment length(s) may be 3,51,535 bps INFO @ Tue, 30 Jun 2020 02:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.10_model.r WARNING @ Tue, 30 Jun 2020 02:04:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:04:25: #2 You may need to consider one of the other alternative d(s): 3,51,535 WARNING @ Tue, 30 Jun 2020 02:04:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:04:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:25: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 02:04:25: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 02:04:25: start model_add_line... INFO @ Tue, 30 Jun 2020 02:04:25: start X-correlation... INFO @ Tue, 30 Jun 2020 02:04:25: end of X-cor INFO @ Tue, 30 Jun 2020 02:04:25: #2 finished! INFO @ Tue, 30 Jun 2020 02:04:25: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:04:25: #2 alternative fragment length(s) may be 3,51,535 bps INFO @ Tue, 30 Jun 2020 02:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.05_model.r WARNING @ Tue, 30 Jun 2020 02:04:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:04:25: #2 You may need to consider one of the other alternative d(s): 3,51,535 WARNING @ Tue, 30 Jun 2020 02:04:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:04:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:04:29: 16000000 INFO @ Tue, 30 Jun 2020 02:04:37: 17000000 INFO @ Tue, 30 Jun 2020 02:04:45: 18000000 INFO @ Tue, 30 Jun 2020 02:04:52: 19000000 INFO @ Tue, 30 Jun 2020 02:05:00: 20000000 INFO @ Tue, 30 Jun 2020 02:05:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:08: 21000000 INFO @ Tue, 30 Jun 2020 02:05:11: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:05:11: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:05:11: #1 total tags in treatment: 21423338 INFO @ Tue, 30 Jun 2020 02:05:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:05:12: #1 tags after filtering in treatment: 21423338 INFO @ Tue, 30 Jun 2020 02:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:12: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:13: #2 number of paired peaks: 113 WARNING @ Tue, 30 Jun 2020 02:05:13: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:13: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:13: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:13: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:13: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:13: #2 predicted fragment length is 51 bps INFO @ Tue, 30 Jun 2020 02:05:13: #2 alternative fragment length(s) may be 3,51,535 bps INFO @ Tue, 30 Jun 2020 02:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.20_model.r WARNING @ Tue, 30 Jun 2020 02:05:13: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:13: #2 You may need to consider one of the other alternative d(s): 3,51,535 WARNING @ Tue, 30 Jun 2020 02:05:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:05:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.10_summits.bed INFO @ Tue, 30 Jun 2020 02:05:19: Done! pass1 - making usageList (470 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.05_summits.bed INFO @ Tue, 30 Jun 2020 02:05:19: Done! pass1 - making usageList (614 chroms): 2 millis pass2 - checking and writing primary data (2552 records, 4 fields): 35 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:05:49: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1847048/SRX1847048.20_summits.bed INFO @ Tue, 30 Jun 2020 02:06:07: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 7 millis CompletedMACS2peakCalling